D-I-TASSER O95428-D4

D-I-TASSER results for O95428-D4

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>O95428 (150 residues)
VLGELTISGLPPTVTVPEGDTARLLCVVAGESVNIRWSRNGLPVQADGHRVHQSPDGTLL
IYNLRARDEGSYTCSAYQGSQAVSRSTEVKVVSPAPTAQPRDPGRDCVDQPELANCDLIL
QAQLCGNEYYSSFCCASCSRFQPHAQPIWQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VLGELTISGLPPTVTVPEGDTARLLCVVAGESVNIRWSRNGLPVQADGHRVHQSPDGTLLIYNLRARDEGSYTCSAYQGSQAVSRSTEVKVVSPAPTAQPRDPGRDCVDQPELANCDLILQAQLCGNEYYSSFCCASCSRFQPHAQPIWQ
Prediction	CCCCCSSSSCCCCSSSSCCCSSSSSSSSSCCCCSSSSSSCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSSCCCCCCCCCCCCCSSSCCCSSSSCSSSSSSSSCCCCCCCSSSCCCCCCCCCCCCCCCC
Confidence	922988982798589948930999999576898799998999947899879993898799935761236899999994896399999999994886348888752241463388008999968438961312431321125888876569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VLGELTISGLPPTVTVPEGDTARLLCVVAGESVNIRWSRNGLPVQADGHRVHQSPDGTLLIYNLRARDEGSYTCSAYQGSQAVSRSTEVKVVSPAPTAQPRDPGRDCVDQPELANCDLILQAQLCGNEYYSSFCCASCSRFQPHAQPIWQ
Prediction	764404036406524154455040404053522403634564505575532433654444445144544444334041543434140403035444435356365533644430504010404236353114110321454445343428
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSSCCCCSSSSCCCSSSSSSSSSCCCCSSSSSSCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCSSSSSSSSSSSCCCCCCCCCCCCCSSSCCCSSSSCSSSSSSSSCCCCCCCSSSCCCCCCCCCCCCCCCC
VLGELTISGLPPTVTVPEGDTARLLCVVAGESVNIRWSRNGLPVQADGHRVHQSPDGTLLIYNLRARDEGSYTCSAYQGSQAVSRSTEVKVVSPAPTAQPRDPGRDCVDQPELANCDLILQAQLCGNEYYSSFCCASCSRFQPHAQPIWQ

2iepA

0.19

0.17

5.58

1.17

DEthreader

LPKAPVITTPLETVDALVEEVATFMCAVESYPPEISWTRNKILIKLFDTRYSIRENQLLTILSVEDSDDGIYCCTANNGVGAVESCGALQVKMKPKI----WIKGDSA-L--RENSRIAVL-S-LRIHNVQKED-AGQYR-KLVKL----

2iepA

0.16

5.32

1.04

SPARKS-K

LPKAPVITTPLETVDALVEEVATFMCAVESYPPEISWTRNKILIKLFDTRYSIRENQLLTILSVEDSDDGIYCCTANNGGGAVESCGALQVKMKPKITEGLKAVLPCTTMGWIKGDSALRERIAVLESGAGQYRCVAKNSLGTAYSKLVK

3pxjA

0.19

0.18

5.83

0.66

MapAlign

AAHPPEIIRKPQNQGVRVGGVASFYCAARGDPPSIVWRKNGKKVSGTQSRYTVLGISILRIEPVRAGDDAPYECVAENGVGAVSADATLTIYEGMTCKAIGNPTPNIYWIKNQTKVDMSNPRYSLKDGFLQIEYECVAENSMGTE-----

3pxjA

0.19

6.04

0.39

CEthreader

AAHPPEIIRKPQNQGVRVGGVASFYCAARGDPPSIVWRKNGKKVSGTQSRYTVLGISILRIEPVRAGDDAPYECVAENGVGAVSADATLTIYEGDKTPAGFPVITQGPGTRVIEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPRYS

2eo9A

0.27

0.21

6.33

1.01

MUSTER

SSGPPVIRQGPVNQTVAVDGTFVLSCVATGSPPTILWRKDGVLVSTQDSRIKQLENGVLQIRYAKLGDTGRYTCIASTPSGEATWSAYIEVQEFGVPVQPPRPTDPNLIPSAP-------------------------------------

3b43A

0.16

5.32

0.48

HHsearch

AMEPPYFIEPLEHVEAAIGEPITLQCKVDGTPIRIAWYKEHTKLRSAPAYKMQFKNASLVINKVDHSDVGEYTCKAENSVGAVASSAVLVIKEPPSETLGFPVAFECRINGWYKDGELLKDDAQTDQSHVGQYNCSASNPLGTASSSTLS

3lafA4

0.29

0.17

5.29

1.41

FFAS-3D

LHRQLYFLQRPSNVIAIEGKDAVLECCVSGYPPSFTWLRGEEVIQLRSKKYSLLGGSNLLISNVTDDDSGTYTCVVTYKNENISASAELTV-----------------------------------------------------------

7cegA

0.20

0.19

6.18

0.47

EigenThreader

PRGFPTIDMGPQLKVVERTRTATMLCAASGPDPEITWFKDFLPVDTSNNNQLRSESIGAQIEQSEESDQGKYECVATNSAGTRYSAPANLYVLGAEDLTPEDDMPIGRNVLELNDVRTCVAMSTLGVIEAIAQITV------KALPKPPG

2rikA

0.19

0.17

5.37

1.94

CNFpred

AMAPPFFDLKPVSVDLALGESGTFKCHVTGTPIKITWAKDNREIRPGNYKMTLVNTATLTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQEPPRFIKKLEPSRIVKQD------------------EHTRYECKIGGS--PEIKVLWY

7ahsA

0.20

0.17

5.53

1.17

DEthreader

LKDEPAWERHLQDVTLKEGQTCTMTCQFSVPNVKSEWFRNGRILKPQG-RHKTEVEHKLTIADVRAEDQGQYTCKYE----DLETSAELRIEAEPIQFT-KR--IQNIAF-WYKGPTEL-------TESQ-KYNFR-ND----RCHYSVI

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7376

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3pxjA	0.70	2.59	0.190	0.827	model1_3pxjA.pdb.gz
2	3pxhA	0.70	2.87	0.179	0.833	model1_3pxhA.pdb.gz
3	7cegA	0.68	3.02	0.171	0.820	model1_7cegA.pdb.gz
4	6iaaA	0.66	3.36	0.168	0.827	model1_6iaaA.pdb.gz
5	4pbxA	0.66	2.96	0.143	0.800	model1_4pbxA.pdb.gz
6	2yd9A	0.65	2.66	0.138	0.773	model1_2yd9A.pdb.gz
7	5noiA	0.61	2.23	0.150	0.687	model1_5noiA.pdb.gz
8	5i99A	0.61	2.79	0.165	0.727	model1_5i99A.pdb.gz
9	3lafA	0.61	2.99	0.252	0.760	model1_3lafA.pdb.gz
10	2cqvA	0.60	2.28	0.159	0.680	model1_2cqvA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0004872	0.69	receptor activity
GO:0099600	0.64	transmembrane receptor activity
GO:0038023	0.64	signaling receptor activity
GO:0004888	0.63	transmembrane signaling receptor activity
GO:0008046	0.58	axon guidance receptor activity
GO:0003824	0.51	catalytic activity
GO:0042802	0.50	identical protein binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.95	single-organism process
GO:0009987	0.93	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0065007	0.82	biological regulation
GO:0032502	0.82	developmental process
GO:0050789	0.81	regulation of biological process
GO:0050794	0.80	regulation of cellular process
GO:0044767	0.72	single-organism developmental process
GO:0048856	0.71	anatomical structure development
GO:0016043	0.65	cellular component organization
GO:0007165	0.65	signal transduction
GO:0051239	0.64	regulation of multicellular organismal process
GO:0051128	0.64	regulation of cellular component organization
GO:0050793	0.64	regulation of developmental process
GO:0048518	0.64	positive regulation of biological process
GO:2000026	0.63	regulation of multicellular organismal development
GO:0045595	0.63	regulation of cell differentiation
GO:0051960	0.62	regulation of nervous system development
GO:0048522	0.62	positive regulation of cellular process
GO:0007166	0.62	cell surface receptor signaling pathway
GO:0007155	0.62	cell adhesion
GO:0048583	0.61	regulation of response to stimulus
GO:0022603	0.61	regulation of anatomical structure morphogenesis
GO:0010975	0.61	regulation of neuron projection development
GO:0008037	0.61	cell recognition
GO:0098609	0.60	cell-cell adhesion
GO:0048519	0.60	negative regulation of biological process
GO:0022604	0.60	regulation of cell morphogenesis
GO:0050770	0.59	regulation of axonogenesis
GO:0008038	0.59	neuron recognition
GO:0048869	0.57	cellular developmental process
GO:0007156	0.57	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0048585	0.56	negative regulation of response to stimulus
GO:0051240	0.55	positive regulation of multicellular organismal process
GO:0051130	0.55	positive regulation of cellular component organization
GO:0051094	0.55	positive regulation of developmental process
GO:0045597	0.55	positive regulation of cell differentiation
GO:0040012	0.55	regulation of locomotion
GO:0009653	0.55	anatomical structure morphogenesis
GO:0006928	0.55	movement of cell or subcellular component
GO:0035385	0.54	Roundabout signaling pathway
GO:0032102	0.54	negative regulation of response to external stimulus
GO:0016199	0.54	axon midline choice point recognition
GO:0010976	0.54	positive regulation of neuron projection development
GO:0010770	0.54	positive regulation of cell morphogenesis involved in differentiation
GO:0009888	0.54	tissue development
GO:0050925	0.53	negative regulation of negative chemotaxis
GO:0050772	0.53	positive regulation of axonogenesis
GO:0060429	0.50	epithelium development
GO:0035295	0.50	tube development

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.95	cell part
GO:0044424	0.64	intracellular part
GO:0044425	0.49	membrane part
GO:0044444	0.48	cytoplasmic part
GO:0044459	0.44	plasma membrane part
GO:0016021	0.42	integral component of membrane
GO:0044421	0.41	extracellular region part
GO:0043226	0.41	organelle
GO:0044422	0.39	organelle part
GO:0016020	0.39	membrane
GO:0005887	0.36	integral component of plasma membrane
GO:0043227	0.34	membrane-bounded organelle
GO:0097458	0.31	neuron part
GO:0043229	0.31	intracellular organelle

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.275	2wwmD	0.586	1.31	0.245	0.627	2.7.11.1	38,73,75,84
2	0.194	2eo1A	0.518	2.41	0.196	0.593	2.7.11.1	51,86
3	0.171	1wvzA	0.475	2.90	0.185	0.613	2.7.10.1	26,36,40,73
4	0.148	2rq8A	0.474	2.92	0.170	0.607	2.7.11.1	14,46
5	0.115	2edhA	0.541	1.65	0.200	0.600	2.7.11.1	86

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.04	1tlk0	0.600	0.89	0.226	0.620	1.20	III	complex1.pdb.gz	1,3,6,29,31,32,34,35,36,44,53,55,56
2	0.03	3dxaE	0.573	3.13	0.130	0.727	0.76	III	complex2.pdb.gz	40,41,71,73,74,85,86
3	0.02	3h9sE	0.593	3.12	0.115	0.747	0.73	III	complex3.pdb.gz	31,79,80,81,82
4	0.02	1evt3	0.583	2.35	0.122	0.660	0.66	III	complex4.pdb.gz	15,16,17,90,92
5	0.02	1e0o3	0.581	2.36	0.116	0.660	0.67	III	complex5.pdb.gz	13,14,15,16,17,90

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.